ESRI UC in San Diego on July 16, 2014

Toolboxes Motivated by Papers

  1. Halpern et al 2008 Science: Cumulative Impacts

  2. Halpern et al 2012 Nature: Ocean Health Index

Cumulative Impacts

Pressures (n=17)

  • Pollution: fertilizer, pesticides, impervious surfaces, population density, ship traffic and ports

  • Fishing Pressure: pelagic low-bycatch, pelagic high-bycatch, demersal destructive, demersal non-destructive low-bycatch, demersal non-destructive high-bycatch, artisanal

  • Climate Change: sea temperature anomoly, ultraviolet radiation, ocean acidification, sea level rise (new)

  • Other: invasive species, oil rigs, shipping

  • 1 km2 pixels in Mollweide projection. Download at nceas.ucsb.edu/globalmarine

Ecosystems (n=20)

  • Special: coral, seagrass, mangrove, rocky reef, seamounts
  • Bottom Type and Depth: soft or hard by shallow (0-60 m), shelf (60-200 m), slope (200 – 2000 m), deep (>2000 m)
  • Offshore Water Column: pelagic (0 to 60 m in depths > 60 m), deep (60 m to bottom)

Matrix of Weights: Ecosystem x Pressure

Result

Equation

\[ I_C = \sum_{i=1}^{n} \sum_{j=1}^{m} P_i * E_j * w_{i,j} \]

  • \(I_C\) cumulative impact score, per 1km pixel
  • \(P_i\) log-transformed and normalized human pressure [0-1]
  • \(E_j\) presence or absence of ecosystem \(j\) [0,1]
  • \(w_{i,j}\) weight for pressure \(i\) and ecosystem \(j\) [0-3.3]

Tool in Model

Tool Form

SeaSketch Integration

Next

Ocean Health Index

What is a Healthy Ocean?

  • Is it pristine?

  • "A healthy ocean sustainably delivers a range of benefits to people now and in the future."

Dimensions

Toolbox Goals

  • Recalculate OHI globally or regionally using alternative weights, equations, layers, etc.
  • Regionalize based on administrative boundaries finer than EEZ.
  • Visualize results to highlight best opportunities for improving ocean health.
  • Interface with easy-to-use forms for sliding weights and concocting scenarios.
  • Automate with tools for manipulating input layers and calculating OHI scores for sensitivity analyses.

Regionalize

US West Coast Halpern et al (2014) PLoS ONE

Brazil Elfes et al (2014) PLoS ONE

Visualize

Flower

Visualize

Map

Process

Toolbox: Data

Map

Toolbox: Data

Histogram

Toolbox: Goals

Toolbox: Calculate

Toolbox: Report

Toolbox: Report -> Result

Regionalization Strategy

  • examples
  • globally
    • political: Global Administrative Areas (GADM)
    • biogeographic: Marine Ecoregions of the World (MEOW)
    • data:
      • pressures: extract from 1km Cumulative Impact rasters (Halpern et al 2008, Halpern et al in draft)
      • other: weight country values from ohi-global by area / coastal population / … of region
    • populate ohi-[country] scenario repository
    • deploy to ShinyApps.io for interactive website

Scenario files

  • layers.csv, layers/
    • *.csv
  • scenario.R, conf/
    • config.R
    • pressures_matrix.csv, resilience_matrix.csv, resilience_weights.csv
    • goals.csv
    • functions.R
  • spatial/regions_gcs.js
  • launchApp_code.R, launchApp.bat (Win), launchApp.command (Mac)
  • scores.csv
  • results/report.html, /figures

Simulation

For example, calculate Baltic Health Index every year using scenarios bhi1980,..., bhi2014 as folders.

library(ohicore)

for (dir_scenario in sprintf('~/ohibaltic/bhi%d', 1980:2014)){
  setwd(dir_scenario)
  
  conf   = Conf('conf')
  layers = Layers('layers.csv', 'layers')
  scores = CalculateAll(conf, layers)
  
  write.csv(scores, 'scores.csv')
}

Software choices for reproducible science

free, cross-platform, open source, web based:

  • csv (comma-seperated value) data files. ancillary: md, json, shp, geotiff
    • Excel poor with Unicode, file locking. Try OpenOffice instead.
  • R having libraries shiny web application, ggplot2 figures, dplyr data manipulation
  • Github repositories:
    • backup to offsite archive, and rewind changes
    • document changes of code and files with issues and messages
    • collaborate with others and publish to web site

Github Repositories

ohiprep | ohi-[scenario] | ohicore

OHI for Github

For More…